Bioinformatics.org is happy to announce that the members have chosen Desmond Higgins of the University College Dublin (UCD) Conway Institute as the laureate of the 2018 Benjamin Franklin Award in the Life Sciences!

Benjamin Franklin (1706-1790) was one of the most remarkable men of his time. Scientist, inventor, statesman, he freely and openly shared his ideas and refused to patent his inventions. It is the opinion of the founders of Bioinformatics.org that he embodied the best traits of a scientist, and we seek to honor those who share these virtues.

``As we enjoy great Advantages from the Inventions of others, we should be glad of an Opportunity to serve others by any Invention of ours; and this we should do freely and generously.''

The Benjamin Franklin Award for Open Access in the Life Sciences is a humanitarian/bioethics award presented annually by this organization to an individual who has, in his or her practice, promoted free and open access to the materials and methods used in the life sciences.

Click here for more information on Dr. Franklin, from the Franklin Institute.

Sponsors

Laureates

2018 – Desmond HigginsDesmond Higgins has been working on methods and software for DNA and protein sequence alignment since 1985. While at Trinity College, Dublin, he wrote a series of sequence alignment programs called CLUSTAL. He later co-deveoped T Coffee (Tree-based Consistency Objective Function for Alignment Evaluation), and his current research group at the UCD Conway Institute develops new, open source tools for evolutionary biology and the mulitvariate analysis of omics data. As of 2018, he has received more than 100,000 citations since 1990 and has 10 papers with over 1,000 citations each. In 2007, Des was elected to the Royal Irish Academy.

2017 – Rafael IrizarryRafael Irizarry has dedicated his career to developing methods and open source software for helping researchers genomics data. As a Biostatistician, he has made fundamental advances in the science of analyzing large, noisy and biased genomics datasets. His contributions are particularly crucial in an era where archives are filling with tens of thousands of large open datasets; to re-use and combine these in any effective way requires a careful approach that considers technical confounders, batch effects, and other issues. See, for example, his work on Frozen robust multiarray analysis (fRMA) and the Gene Expression Barcode. Rafael is also a contributor to and a leader of the influential Bioconductor project, which has helped to popularize open source software and open software development in the genomics and statistical communities.

2016 – Benjamin LangmeadBenjamin Langmead is one of the most influential and highly cited authors of open source bioinformatics software. His Bowtie read alignment tool and its sequel Bowtie 2 (bowtie-bio.sourceforge.net/bowtie2/index.shtml) are widely used, with more than 10,000 citations between them, and they are used within more than 50 other software tools. Ben also has a series of publications on open source cloud-enabled tools that have collectively pushed back the frontier of what everyday biological researchers can do with large sequencing datasets. All of Ben's software, and all the software from his lab, are free and open source. He has also made available a large collection of open teaching resources that have become very popular (www.langmead-lab.org/teaching-materials/).

2015 – Owen WhiteOwen White has been a leading proponent of open access software since the late 1990's, when he worked as the Director of Bioinformatics at The Institute for Genomic Research (TIGR). At TIGR and in the years since then, he has consistently advocated for the free release of software and of genome sequence data. He led the development of the Comprehensive Microbial Resource (first published in 2001), one of the first and at the time one of the largest open databases of bacterial genome annotation. As a PI of the NIH Human Microbiome Project (HMP) Data Analysis and Coordination Center, Owen has advocated that all data be open access. In recent years his group has developed several influential open-source software systems for genome annotation, including Manatee, Ergatis and the IGS Prokaryotic Annotation Engine.

2014 – Helen M. BermanHelen Berman is awarded the 2014 Benjamin Franklin Award. Helen was a champion of the open access of scientific information at a time when the concept of data sharing was in its infancy. For nearly five-decades, she has been committed to ensuring that the Protein Data Bank (PDB) archive has been a resource created by the community for the community. As head of the Research Collaboratory for Structural Bioinformatics (RCSB), Helen became the Director of the PDB in 1998, and developed the RCSB PDB into a vital and key resource for biology and education. In 2003, she formed the Worldwide PDB with groups in the UK and Japan to ensure that a single PDB archive continues to be freely and publicly available to the global community. Her passion for making structural data accessible and understandable by a broad community has driven the development of other bioinformatics resources, ontologies, and community-driven validation standards. These include the Electron Microscopy Data Bank, a global deposition and retrieval network for cryoEM map, model and associated metadata; the Nucleic Acid Database, a resource for information about nucleic acid structure; and the Structural Biology Knowledgebase, a comprehensive resource that integrates the results of structural biology and genomics efforts with other publicly available biological information to facilitate further research.

2013 – Steven SalzbergSteven Salzberg is awarded the 2013 Benjamin Franklin Award. Steven has made many contributions to open access bioinformatics software, beginning with the pioneering system for bacterial gene finding, Glimmer, and the MUMmer whole-genome alignment package. His group has built a suite of next-generation sequencing tools including Bowtie, TopHat, and Cufflinks, which have been adopted by thousands of scientists around the world, and have collectively been downloaded over 200,000 times. Steven has developed open source software for genome assembly as well, launching the AMOS project that includes many assemblers and assembly utilities. He has publicly advocated for greater sharing of data, and was the co-founder of the Influenza Genome Project, which sequenced thousands of strains of the influenza virus. Steven has also advocated forcefully against both software and gene patents, publishing many commentaries in high-profile journals and on his genomics and Forbes blog sites.

2012 – Heng LiHeng Li is awarded the 2012 Benjamin Franklin Award. Heng has been a fundamental
contributor to widely used open source software. He is known for his essential contributions
to the next generation sequencing (NGS) field with tools like
SAMtools,
BWA, MAQ,
TreeSoft and
TreeFam, that have in many cases been adopted as
standard sequencing analysis tools. Before his involvement in NGS, Heng developed algorithms
for the analysis of gene family evolution, namely
TreeBeST, and he participated
in the TreeFam and Ensembl GeneTrees
databases. He is remarkably active in open forums for bioinformatics like seqanswers.com
and biostars.org, always ready to lend a helping hand to new users in the field. Heng has
also focused in pure research projects, and as an example, he published a fundamental piece
of work in the field of human genetics in the inference of human population history from
individual whole-genome
sequences.

2011 – Jonathan A. EisenJonathan A. Eisen is awarded the 2011 Benjamin Franklin Award. Jonathan uses his
high visibility in social media to advocate for open access by sharing links to discussions,
mentioning open access articles and initiatives, and pushing for the opening up of popular
closed access articles. This culture is shared with his students, who advocate for "open
access" peer reviewing and created a peer-to-peer service for sharing bioinformatics
material (articles, software and datasets). He is the academic editor in chief of
PLoS Biology and voices his
opinions and support for open access publication and open data sharing on his "Tree of Life" blog. In addition to just
voicing his opinion, he also practices what he preaches, by refusing to publish in non-open
access journals. With respect to bioinformatics, he has been involved with many software
packages that are freely available, such as the recent
AMPHORA and
PhyloOTU.
Lastly, Jonathan helped release a new open data sharing tool for scientists called
BioTorrents.
This is just another step in encouraging all scientists to share their data and results
more openly.

2010 – Alex BatemanAlex Bateman is awarded the 2010 Benjamin Franklin Award for leading the freely
available and very useful Pfam,
Rfam and MEROPS
databases at the Wellcome Trust Sanger Institute since moving there in 1997. He was
also the Executive Editor for the open-access
Database issue
of the journal Nucleic Acids Research for many years. Furthermore, Bateman helped
initiate the RNA Families track at the journal
RNA Biology, where a
Wikipedia article is required for each published RNA family.

2009 – Philip E. BournePhilip E. Bourne is awarded the 2009 Benjamin Franklin Award for his numerous and varied contributions to both open access in bioinformatics and computational biology as well as his innovations with the Protein Data Bank (PDB). A past president of the International Society for Computational Biology (ISCB), Bourne is the founding editor-in-chief of PLoS Computational Biology, one of the open-access journals launched by the Public Library of Science. Bourne is also a co-founder (with PLoS) of the website SciVee.tv, which allows scientists across many disciplines to upload videos, lectures, presentations and posters.

2008 – Robert GentlemanRobert Gentleman is awarded the 2008 Benjamin Franklin Award for his work on the R suite of statistical tools and, together with other core members, founding and developing BioConductor, an open-source and open-development software project for the analysis and comprehension of genomic data. More importantly, Robert has a strong ethical view on the meaning of publishing data, with an emphasis on sharing data-transformation methods as well as the underlying data.

2007 – Sean EddySean Eddy is awarded the 2007 Benjamin Franklin Award for the development and free distribution of HMMER, which has revolutionized the use of profile Hidden Markov Models in protein sequence analysis, and for the co-creation of the Pfam database of protein domains and families, which has been an essential counterpart as the basis of genome annotations, family classification systems such as GO, and much of our common language of protein annotation.

2005 – Ewan BirneyEwan Birney is awarded the 2005 Benjamin Franklin Award for his promotion of Open Access in bioinformatics and science. He has been a key developer in the Ensembl and BioPerl projects and a strong advocate for making genome information freely available.

2004 – Lincoln D. SteinLincoln D. Stein is awarded the 2004 Benjamin Franklin Award for his creation of a great number of open-source bioinformatics programs and for championing open-source principals in many venues, including published reviews, lectures, seminars, funding-review panels, and advisory board meetings.

2003 – James KentJames Kent is awarded the 2003 Benjamin Franklin Award for developing GigAssembler, a 10,000 line program that he wrote in a month and then used to assemble the public human genome fragments. This was accomplished before Celera Genomics was able to assemble their private genome, helping to keep the data in the public domain and unrestricted by commercial patents.